A Universal Differential Expression Prediction Tool for Single-Cell and Spatial Genomics Data

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Documentation for package ‘singleCellHaystack’ version 1.0.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

dat.expression	Single cell RNA-seq dataset.
dat.tsne	Single cell tSNE coordingates.
default_bandwidth.nrd	Default function given by function bandwidth.nrd in MASS. No changes were made to this function.
extract_row_dgRMatrix	Returns a row of a sparse matrix of class dgRMatrix. Function made by Ben Bolker and Ott Toomet (see https://stackoverflow.com/questions/47997184/)
extract_row_lgRMatrix	Returns a row of a sparse matrix of class lgRMatrix. Function made by Ben Bolker and Ott Toomet (see https://stackoverflow.com/questions/47997184/)
get_density	Function to get the density of points with value TRUE in the (x,y) plot
get_dist_two_sets	Calculate the pairwise Euclidean distances between the rows of 2 matrices.
get_D_KL	Calculates the Kullback-Leibler divergence between distributions.
get_D_KL_continuous_highD	Calculates the Kullback-Leibler divergence between distributions for the high-dimensional continuous version of haystack.
get_D_KL_highD	Calculates the Kullback-Leibler divergence between distributions for the high-dimensional version of haystack().
get_euclidean_distance	Calculate the Euclidean distance between x and y.
get_grid_points	A function to decide grid points in a higher-dimensional space
get_log_p_D_KL	Estimates the significance of the observed Kullback-Leibler divergence by comparing to randomizations.
get_log_p_D_KL_continuous	Estimates the significance of the observed Kullback-Leibler divergence by comparing to randomizations for the continuous version of haystack.
get_parameters_haystack	Function that decides most of the parameters that will be used during the "Haystack" analysis.
get_reference	Get reference distribution
haystack	The main Haystack function
haystack.data.frame	The main Haystack function
haystack.matrix	The main Haystack function
haystack.Seurat	The main Haystack function
haystack.SingleCellExperiment	The main Haystack function
haystack_2D	The main Haystack function, for 2-dimensional spaces.
haystack_continuous_highD	The main Haystack function, for higher-dimensional spaces and continuous expression levels.
haystack_highD	The main Haystack function, for higher-dimensional spaces.
hclust_haystack	Function for hierarchical clustering of genes according to their expression distribution in 2D or multi-dimensional space
hclust_haystack.data.frame	Function for hierarchical clustering of genes according to their expression distribution in 2D or multi-dimensional space
hclust_haystack.matrix	Function for hierarchical clustering of genes according to their expression distribution in 2D or multi-dimensional space
hclust_haystack_highD	Function for hierarchical clustering of genes according to their distribution in a higher-dimensional space.
hclust_haystack_raw	Function for hierarchical clustering of genes according to their distribution on a 2D plot.
kde2d_faster	Based on the MASS kde2d() function, but heavily simplified; it's just tcrossprod() now.
kmeans_haystack	Function for k-means clustering of genes according to their expression distribution in 2D or multi-dimensional space
kmeans_haystack.data.frame	Function for k-means clustering of genes according to their expression distribution in 2D or multi-dimensional space
kmeans_haystack.matrix	Function for k-means clustering of genes according to their expression distribution in 2D or multi-dimensional space
kmeans_haystack_highD	Function for k-means clustering of genes according to their distribution in a higher-dimensional space.
kmeans_haystack_raw	Function for k-means clustering of genes according to their distribution on a 2D plot.
plot_compare_ranks	plot_compare_ranks
plot_gene_haystack	Visualizing the detection/expression of a gene in a 2D plot
plot_gene_haystack.data.frame	Visualizing the detection/expression of a gene in a 2D plot
plot_gene_haystack.matrix	Visualizing the detection/expression of a gene in a 2D plot
plot_gene_haystack.Seurat	Visualizing the detection/expression of a gene in a 2D plot
plot_gene_haystack.SingleCellExperiment	Visualizing the detection/expression of a gene in a 2D plot
plot_gene_haystack_raw	Visualizing the detection/expression of a gene in a 2D plot
plot_gene_set_haystack	Visualizing the detection/expression of a set of genes in a 2D plot
plot_gene_set_haystack.data.frame	Visualizing the detection/expression of a set of genes in a 2D plot
plot_gene_set_haystack.matrix	Visualizing the detection/expression of a set of genes in a 2D plot
plot_gene_set_haystack.Seurat	Visualizing the detection/expression of a set of genes in a 2D plot
plot_gene_set_haystack.SingleCellExperiment	Visualizing the detection/expression of a set of genes in a 2D plot
plot_gene_set_haystack_raw	Visualizing the detection/expression of a set of genes in a 2D plot
plot_rand_fit	plot_rand_fit
plot_rand_fit.haystack	plot_rand_fit
plot_rand_KLD	plot_rand_KLD
read_haystack	Function to read haystack results from file.
show_result_haystack	show_result_haystack
show_result_haystack.haystack	show_result_haystack
write_haystack	Function to write haystack result data to file.